Theoretical Study On The Enzymatic Transformation And Atmospheric Degradation Mechanisms Of Typical Environmental Organic Pollutants

Enzymes are biological macromolecules with specific spatial conformation and catalytic activity in living organisms.Because of their specific,efficient and mild reaction conditions.Biological enzymes are widely used in medical synthesis and industrial and agricultural production.Facing China's increasingly serious environmental pollution problems,the application of enzymes in dealing with environmental issue has begun to attract more and more scholars' attention.People can use the characteristics of efficient and specific degradation of biological enzymes to degrade organic pollutants in the environment and alleviate the ecosystem crisis.At the same time,the biological enzymes technology can also be applied to the production process of catalytic synthesis or fermentation to reduce the pollution emissions in the synthesis process.At present,the experimental methods for studying biological enzymes are increasingly abundant,but these experimental studies cannot describe the detailed process of enzyme-catalyzed reactions,which also limits our understanding of enzymology and limits the application of enzyme catalysis.The quantum mechanics/molecular mechanics(QM/MM)approaches can describe the enzymatic reaction process at the atomic level,and has gradually become an indispensable and effective means to study the enzyme catalytic reaction.In this dissertation,the molecular dynamics(MD)method and QM/MM approaches were used to study the catalytic reaction mechanisms of biphenyl,Halogenated biphenyls and 3-chlorocatechol in enzymatic systems.The details of the enzyme catalytic reaction processes were revealed,which verified,explained and supplemented the related experimental results.Describes the detailed information of the enzyme degradation system,reveals the reaction characteristics of the enzyme and promotes its application in the environmental field.1.Mechanism of biphenyl dehydrogenase catalyzing degradation of biphenylCis-2,3-Dihydro-2,3-dihydroxybiphenyl dehydrogenase(BphB)belongs to the short-chain dehydrogenase/reductase(SRD)family that are widely found in nature.BphB need to rely on the coenzyme NAD(nicotinamide adenine dinucleotide,oxidation state)to synergistically catalyze biphenyl,and remove two hydrogen atoms on the 2-position of biphenyl.BphB plays an important catalytic role in the degradation of biphenyl,halogenated biphenyl.As a widely used organic synthesis precursor in chemical and pharmaceutical industries,biphenyl has a large residual amount in the environment and has an important impact on human health.In this dissertation,the enzymatic mechanism of biphenyl was studied with the aid of a combined quantum mechanics/molecular mechanics method.The following results are obtained:in addition to the biphenyl dehydrogenase BphB,coenzyme NAD is also involved in the catalytic degradation process of biphenyl.The research conclusions explain and verify the experimental mechanism,that is,the dehydrogenation process of biphenyl is a one-step synergistic reaction process,and two hydrogens in biphenyl are transferred to Tyr155 and coenzyme NAD+,respectively.In addition,The electrostatic influence analysis reveals that Ser142 facilitates the degradation reaction and Lys159 and Asnl43 suppress the process.As a consequence,the present dissertation can provide a theoretical basis for subsequent BphB mutation modification experiments.The dissertation also deepened the understanding of BphB catalytic degradation of biphenyl,which can be used as a model to study the degradation of other polyhalogenated biphenyls.2.Substituent effects of biphenyl dehydrogenase in the degradation of halogenated biphenylsChloroaromatic compounds have received attention due to their potential toxicity,persistence and bioaccumulation.Polyhalogenated biphenyls include polyfluorobiphenyls(PFBs),polychlorinated biphenyls(PCBs),polybrominated biphenyls(PBBs)and polyiodobiphenyls(PIBs).Among them,polychlorinated biphenyls and polybrominated biphenyls have been globally used for industrial purposes until they were found highly toxic,mutagenic and carcinogenic to humans.The residual amount of polychlorinated biphenyls in the environment is more than 280,000 tons,and this situation has caused great concern.In this dissertation,we investigated the fluorined,chlorined,bromined,and iodined substitutions effect of BphB(cis-2,3-dihydro-2,3-dihydroxybiphenyl-2,3-dehydrogenase)catalyzed degradation of halogenated biphenyls by using the state-of-the-art quantum mechanics/molecular mechanics method.The computing results reveal that Biphenyl dehydrogenase BphB can efificiently degrade biphenyl and halogenated biphenyl,and the corresponding Boltzmann-weighted average degradation barriers are all lower than the unsubstituted cis-2,3-dihydro-2,3-dihydroxybiphenyl,except for chlorined biphenyl.The results also can deepen the understanding of the BphB catalyzed degradation processes and can serve as the model for studying other polyhalogenated biphenyls.The electrostatic influence analysis reveals that serine 142 facilitates the degradation reaction and residue asparagine143 suppresses the degradation reaction,which may assist searching for new experimental mutation targets for future enzyme modification.The conclusions of this study can provide a theoretical reference for the study of degradation of other types of polyhalogenated biphenyls.3.Mechanism of chloromuconolactone dehalogenase catalyzing degradation of 3-chlorocatecholChlorinated aromatic compounds are of environmental concern because of their potential toxicity,persistence,and tendency of bioaccumulation and thus is responsible for the high environmental relevance of this heterogeneous group of substances.Chlorinated aromatic compounds in the environment are mainly derived from pesticides,herbicides,chlorinated solvents and industrial wastes.The pollution caused by chlorinated aromatic compounds has become very serious,and the degradation of chlorinated aromatic compounds in the environment has become an important issue of environmental research.ClcF belongs to muconolactone isomerase(MLI)family.Because of chloromuconolactone dehalogenase(ClcF)has broad specificity for substrates and strong ability to degrade chloroaromatic compounds.It has broad application prospects in the degradation of chlorinated aromatic compounds.In this dissertation,the active site residues of ClcF are formed by two monomers.3-chlorocatechol was used as an example to simulate the degradation reaction mechanism by using QM/MM method.The computing results reveal the catalytic degradation of 3-chlorocatechol by chloromuconate dehalogenase ClcF is completed in two steps reaction,namely the hydrogen transfer step and the synergistic elimination of chlorine,and the second step is rate-determining step.Amino acid Glu27 in the active site of ClcF is deprotonated,acts as the proton acceptor in the degradation process.The electrostatic influence analysis reveals that Arg45 suppresses the degradation reaction,which may assist searching for new experimental mutation targets for future enzyme modification to enhance the catalytic efficiency of chloromuconate dehalogenase ClcF.4.Atmospheric oxidation of 4-hydroxy-2-butanoneHydroxycarbonyls are vital oxygenated volatile organic compounds(OVOCs)and make strongly contribute to the formation of tropospheric ozone and photochemical smog.As typical OVOCs,4-hydroxy-2-butanone(CH3CO-CH2CH2OH)is wildly used in the pharmaceutical industries,fine chemicals manufacture and the foods.Due to the high vapor pressure in the atmosphere,4H2B can be easy emitted into the atmosphere during their production and use processes,and inevitably causing the formation of many secondary pollutants,such as photochemical smog and tropospheric ozone.In this dissertation,high-accuracy quantum chemical calculations based on MPWB1K/6-311+G(3df,2p)//MPWB1K/6-31+G(d,p)level was employed in study atmospheric oxidation degradation of 4-hydroxy-2-butanone initiated by OH radicals.The possible reaction pathways,intermediates and products in the atmospheric degradation process of 4-hydroxy-2-butanone with OH radicals were proposed and discussed.The total and site-specific reaction rate constants were calculated by employing POLYRATE 9.7 program.The calculated overall rate constant is 1.64×1012 cm3 molecule-1 s-1 at 298K.In hydrogen abstraction pathways,the H ion from the C3-H bond in 4-hydroxy-2-butanone is the most energetically favorable because of the high exothermicity and lowest barrier.The main products of the 4-hydroxy-2-butanone atmospheric degradation are formaldehyde,peroxy radicals and unsaturated aldehyde ketone compounds.Understanding degradation mechanism of 4-hydroxy-2-butanone can deepen our understanding on the degradation processes of OVOCs in the atmosphere.